just adding nyaplot gem (not even calling) gives me an error on osx (yosemite, 10.10.5) #55

tansaku · 2015-11-11T17:18:04Z

 $ ruby lib/correlation.rb 
/Users/tansaku/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.7/lib/iruby/utils.rb:8:in `display': undefined method `session' for nil:NilClass (NoMethodError)
    from /Users/tansaku/.rvm/gems/ruby-2.2.3/gems/nyaplot-0.1.6/lib/nyaplot/core.rb:45:in `init_iruby'
    from /Users/tansaku/.rvm/gems/ruby-2.2.3/gems/nyaplot-0.1.6/lib/nyaplot/core.rb:48:in `<module:Nyaplot>'
    from /Users/tansaku/.rvm/gems/ruby-2.2.3/gems/nyaplot-0.1.6/lib/nyaplot/core.rb:3:in `<top (required)>'
    from /Users/tansaku/.rvm/gems/ruby-2.2.3/gems/nyaplot-0.1.6/lib/nyaplot.rb:4:in `require_relative'
    from /Users/tansaku/.rvm/gems/ruby-2.2.3/gems/nyaplot-0.1.6/lib/nyaplot.rb:4:in `<top (required)>'
    from /Users/tansaku/.rvm/rubies/ruby-2.2.3/lib/ruby/2.2.0/rubygems/core_ext/kernel_require.rb:128:in `require'
    from /Users/tansaku/.rvm/rubies/ruby-2.2.3/lib/ruby/2.2.0/rubygems/core_ext/kernel_require.rb:128:in `rescue in require'
    from /Users/tansaku/.rvm/rubies/ruby-2.2.3/lib/ruby/2.2.0/rubygems/core_ext/kernel_require.rb:39:in `require'
    from /Users/tansaku/.rvm/gems/ruby-2.2.3/gems/daru-0.1.1/lib/daru.rb:45:in `block in create_has_library'
    from /Users/tansaku/.rvm/gems/ruby-2.2.3/gems/daru-0.1.1/lib/daru/plotting/vector.rb:39:in `<top (required)>'
    from /Users/tansaku/.rvm/rubies/ruby-2.2.3/lib/ruby/2.2.0/rubygems/core_ext/kernel_require.rb:54:in `require'
    from /Users/tansaku/.rvm/rubies/ruby-2.2.3/lib/ruby/2.2.0/rubygems/core_ext/kernel_require.rb:54:in `require'
    from /Users/tansaku/.rvm/gems/ruby-2.2.3/gems/daru-0.1.1/lib/daru/vector.rb:5:in `<top (required)>'
    from /Users/tansaku/.rvm/rubies/ruby-2.2.3/lib/ruby/2.2.0/rubygems/core_ext/kernel_require.rb:54:in `require'
    from /Users/tansaku/.rvm/rubies/ruby-2.2.3/lib/ruby/2.2.0/rubygems/core_ext/kernel_require.rb:54:in `require'
    from /Users/tansaku/.rvm/gems/ruby-2.2.3/gems/daru-0.1.1/lib/daru.rb:70:in `<top (required)>'
    from /Users/tansaku/.rvm/rubies/ruby-2.2.3/lib/ruby/2.2.0/rubygems/core_ext/kernel_require.rb:54:in `require'
    from /Users/tansaku/.rvm/rubies/ruby-2.2.3/lib/ruby/2.2.0/rubygems/core_ext/kernel_require.rb:54:in `require'
    from /Users/tansaku/.rvm/gems/ruby-2.2.3/gems/statsample-2.0.1/lib/statsample.rb:25:in `<top (required)>'
    from /Users/tansaku/.rvm/rubies/ruby-2.2.3/lib/ruby/2.2.0/rubygems/core_ext/kernel_require.rb:128:in `require'
    from /Users/tansaku/.rvm/rubies/ruby-2.2.3/lib/ruby/2.2.0/rubygems/core_ext/kernel_require.rb:128:in `rescue in require'
    from /Users/tansaku/.rvm/rubies/ruby-2.2.3/lib/ruby/2.2.0/rubygems/core_ext/kernel_require.rb:39:in `require'
    from lib/correlation.rb:2:in `<main>'

first two lines of the file:

``ruby
require 'iruby'
require 'statsample'


if I remove the nyaplot gem everything runs fine :-(

The text was updated successfully, but these errors were encountered:

v0dro · 2015-11-12T08:10:47Z

@domitry will need to take a look here.

If your requirement is urgent, you might want to use the Gnuplotrb gem for now.

domitry · 2015-11-13T02:58:29Z

It seems that dependency of iruby , ex: rczmq or iruby itself caused your problem.
Can you try the code below?

txt = "alert(\"Hello, world!\");"
IRuby.display(IRuby.javascript(txt))

tansaku · 2015-11-13T07:28:33Z

@domitry thanks - same error

2.2.3 :001 > txt = "alert(\"Hello, world!\");"
 => "alert(\"Hello, world!\");" 
2.2.3 :002 > IRuby.display(IRuby.javascript(txt))
NoMethodError: undefined method `session' for nil:NilClass
    from /Users/tansaku/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.7/lib/iruby/utils.rb:8:in `display'
    from (irb):2
    from /Users/tansaku/.rvm/rubies/ruby-2.2.3/bin/irb:15:in `<main>'

is there a display variable or something I need to set?

domitry · 2015-11-13T08:06:34Z

Oops, I just noticed that you execute the script on the shell, not browser.
There are two solutions:

Remove the line require 'iruby'.
run iruby notebook and edit the code on your browser.

or

Remove the line require 'iruby'.
Run ruby script.rb.

domitry · 2015-11-13T08:09:04Z

Please re-open this if my suggestion not work :)

tansaku · 2015-11-17T07:54:40Z

thanks @domitry

iruby notebook fails for me like this (assuming I'm actually trying to make a graph ds.plot type: :histogram):

→ iruby notebook
Traceback (most recent call last):
  File "/usr/local/bin/ipython", line 11, in <module>
    sys.exit(start_ipython())
  File "/Library/Python/2.7/site-packages/IPython/__init__.py", line 118, in start_ipython
    return launch_new_instance(argv=argv, **kwargs)
  File "/Library/Python/2.7/site-packages/traitlets/config/application.py", line 591, in launch_instance
    app.initialize(argv)
  File "<decorator-gen-111>", line 2, in initialize
  File "/Library/Python/2.7/site-packages/traitlets/config/application.py", line 75, in catch_config_error
    return method(app, *args, **kwargs)
  File "/Library/Python/2.7/site-packages/IPython/terminal/ipapp.py", line 305, in initialize
    super(TerminalIPythonApp, self).initialize(argv)
  File "<decorator-gen-7>", line 2, in initialize
  File "/Library/Python/2.7/site-packages/traitlets/config/application.py", line 75, in catch_config_error
    return method(app, *args, **kwargs)
  File "/Library/Python/2.7/site-packages/IPython/core/application.py", line 386, in initialize
    self.parse_command_line(argv)
  File "/Library/Python/2.7/site-packages/IPython/terminal/ipapp.py", line 300, in parse_command_line
    return super(TerminalIPythonApp, self).parse_command_line(argv)
  File "<decorator-gen-4>", line 2, in parse_command_line
  File "/Library/Python/2.7/site-packages/traitlets/config/application.py", line 75, in catch_config_error
    return method(app, *args, **kwargs)
  File "/Library/Python/2.7/site-packages/traitlets/config/application.py", line 487, in parse_command_line
    return self.initialize_subcommand(subc, subargv)
  File "<decorator-gen-3>", line 2, in initialize_subcommand
  File "/Library/Python/2.7/site-packages/traitlets/config/application.py", line 75, in catch_config_error
    return method(app, *args, **kwargs)
  File "/Library/Python/2.7/site-packages/traitlets/config/application.py", line 418, in initialize_subcommand
    subapp = import_item(subapp)
  File "/Library/Python/2.7/site-packages/ipython_genutils/importstring.py", line 31, in import_item
    module = __import__(package, fromlist=[obj])
ImportError: No module named notebook.notebookapp

but the nyaplot gem by itself won't blow up with the iruby require removed.

I guess my basic iruby (ipython?) installation is not working? I guess I may just have to bang my head against that for a while :-/ Any tips?

If I remove require 'iruby' I get uninitialized constant Nyaplot::Frame::IRuby

I will also try https://github.com/dilcom/gnuplotrb as @v0dro suggests ...

domitry · 2015-11-17T07:59:51Z

Yes, maybe you failed to install IPython. Can you try to run ipython notebook?

domitry · 2015-11-17T08:07:30Z

Using plot.export_html("foo.html") instead of plot.show will solve uninitialized constant Nyaplot::Frame::IRuby issue.

Plot#show works only on IRuby notebook.

Example: https://github.com/domitry/nyaplot/blob/v2/examples/rb/basic.rb

tansaku · 2015-11-17T08:09:29Z

@domitry I could not - got the same error. Trying to do pip install notebook I get permissions error. In frustration I just sudo'd it, so now both ipython notebook and iruby notebook work, bringing up notebooks in the browser. I tried running my script from the command line:

ruby lib/correlation.rb

but I still get the same error as before if the iruby and nyaplot gems are required - whether or not I try and draw anything.

I can view my script in the iruby notebook view through the browser, but cannot immediately see how to run it there ...

domitry · 2015-11-17T08:13:13Z

Run iruby notebook and click New -> Ruby *.*.* then new window will open on your browser.

Then copy lines in correlation.rb and paste them to boxes on the notebook just like the movie:
https://www.youtube.com/watch?v=ZxjqsIluM88

tansaku · 2015-11-17T08:19:31Z

thanks @domitry - right - I have the running - really appreciate your help. Only difficulty now, is that in the notebook everything is running relative to the location of the iruby gem, rather than my project folder, which I was requiring some other classes relatively, and loading files from:

/Users/tansaku/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.7/lib/iruby/

Do I need to hard code all my paths relative to root, or is there a way to make the iruby notebook run from a particular point on the file system? My googles and github issue searches "iruby require_relative" are drawing blanks ATM.

tansaku · 2015-11-17T08:21:36Z

in the meantime I hardcoded all the paths relative to root, but then I get:

LoadError: cannot load such file -- nyaplot

works fine if I remove the require 'nyaplot'

domitry · 2015-11-17T08:30:53Z

Maybe require_relative works relative to the directory where you ran iruby notebook.
If require 'nyaplot' fails, something I don't know is going in your PC.

tansaku · 2015-11-17T13:13:11Z

thanks so much for your ongoing help on this @domitry. I would expect require_relative to work relative to the directory where I run iruby notebook but it seems like it is running relative to the gem.

I'm on OSX rather than PC, but so I followed your earlier advice, and I have https://github.com/domitry/nyaplot/blob/v2/examples/rb/basic.rb working generating graphs that I can view in html files.

It seems like require nyaplot is now working (I did restart the computer as well and that might have helped). So now my correlation script runs and attempts to draw the graph, but the graph is blank and I get:

Javascript error adding output!
Error: Mismatched anonymous define() module: [object Object] http://requirejs.org/docs/errors.html#mismatch
See your browser Javascript console for more details.

and looking in the javascript console I get:

Failed to load resource: the server responded with a status of 404 (Not Found)
main.min.js:30434 ipywidgets package not installed.  Widgets are not available.
main.min.js:23181 Session: kernel_created (32eb103a-2a19-4ded-a23d-c6e2990d82e2)
main.min.js:22502 Starting WebSockets: ws://localhost:8888/api/kernels/0bb0eacb-ef01-4513-b0ce-84573887c498
main.min.js:22160 Kernel: kernel_connected (0bb0eacb-ef01-4513-b0ce-84573887c498)
main.min.js:22160 Kernel: kernel_ready (0bb0eacb-ef01-4513-b0ce-84573887c498)
(program):12 finished loading d3
(program):12 finished loading downloadable
(program):25 Finished loading Nyaplotjs
main.min.js:20056 Error: Mismatched anonymous define() module: [object Object](…)

so maybe I need ipywidgets ... or maybe the basic script operation I'm following needs changing. I'm following the tutorial here:

http://v0dro.github.io/blog/2014/11/25/data-analysis-in-ruby-basic-data-manipulation-and-plotting/

In particular I'm trying to print out something thats a DaruFrame

I've installed ipywidgets, and now the error in the js console is just:

Uncaught Error: Mismatched anonymous define() module: [object Object]
http://requirejs.org/docs/errors.html#mismatch

but I think I see how I can use nyaplot to generate the html graphs for me - just wanted to add all the above to record the process I was going through. Please don't feel you need to offer any more help, unless you feel like there is something important I have missed in my exploration :-)

tansaku changed the title ~~just adding nyaplot gem (not even calling) gives me an error on osx~~ just adding nyaplot gem (not even calling) gives me an error on osx (yosemite, 10.10.5) Nov 11, 2015

tansaku mentioned this issue Nov 11, 2015

iruby-0.2.7/lib/iruby/utils.rb:8:in display': undefined method session' for nil:NilClass (NoMethodError) SciRuby/iruby#48

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domitry closed this as completed Nov 13, 2015

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just adding nyaplot gem (not even calling) gives me an error on osx (yosemite, 10.10.5) #55

just adding nyaplot gem (not even calling) gives me an error on osx (yosemite, 10.10.5) #55

tansaku commented Nov 11, 2015

v0dro commented Nov 12, 2015

domitry commented Nov 13, 2015

tansaku commented Nov 13, 2015

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tansaku commented Nov 17, 2015

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tansaku commented Nov 17, 2015

just adding nyaplot gem (not even calling) gives me an error on osx (yosemite, 10.10.5) #55

just adding nyaplot gem (not even calling) gives me an error on osx (yosemite, 10.10.5) #55

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tansaku commented Nov 11, 2015

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tansaku commented Nov 13, 2015

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